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Administering Pathway Tools

Administering Pathway Tools. Obtaining Pathway Tools. Free to non-commercial organizations To obtain license agreement go to BioCyc.org and click on Software/Database Download Follow Installation Guide ptools-local directory Locate in common directory

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Administering Pathway Tools

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  1. Administering Pathway Tools

  2. Obtaining Pathway Tools • Free to non-commercial organizations • To obtain license agreement go to BioCyc.org and click on Software/Database Download • Follow Installation Guide • ptools-local directory • Locate in common directory • PGDBs created by all users who use this ptools installation • PGDBs downloaded via the registry • ptools-init.dat for this ptools installation

  3. New Pathway Tools Releases • Major releases = External software releases • Twice per year • Announced on ptools-users mailing list • Minor releases twice per year affect only our BioCyc.org Web site and flatfile distributions • We support one prior release only • Releases announced on ptools-users@ai.sri.com • Read release notes at • http://brg.ai.sri.com/ptools/release-notes.html • Install process: • Upgrade schema of your DB (software assisted)

  4. PGDB Storage:File or Relational Database • File storage: • Advantages: • No RDBMS installation and configuration • Disadvantages: • Must be loaded and saved in its entirety • No transaction history • No concurrent access for multiple users • Oracle/MySQL storage: • Advantages: • Faster read access, faster saves • Concurrent update access for multiple users • Stores history of all PGDB updates • Disadvantages: • RDBMS must be installed and configured

  5. Multiuser Access to PGDBs • PGDB stored within one Oracle or MySQL server • Each curator installs PTools on their workstation • Different curators can use different software platforms • Workstations query RDBMS server via internet • Local disk cache speeds access • For each frame access, PTools queries • In-memory cache, disk cache, RDBMS server • After curator saves changes, all changes made by other users are loaded into curator’s session

  6. How to Release a PGDB? • Decide on release frequency and schedule • Don’t wait until it’s perfect to release it! • Freeze curation for 1 week • Quality assurrance • Run consistency checker • Tools -> Consistency Checker • Also updates organism-summary statistics • Update publications, authors in organism frame • Update via Organism editor • Create new version of PGDB • ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelot • Edit against the new version, release the old version • Author release notes • Register PGDB in SRI PGDB registry • Will allow SRI to include it in BioCyc

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